Downloads
We can announce finally we have tappAS published. To cite us you can do it using the following text:
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Ana Alastrue-Agudo, Pablo Bonilla, Jeremy Newman, Lauren McIntyre, Victoria Moreno-Manzano, Ana Conesa
Genome Biology; doi: https://doi.org/10.1186/s13059-020-02028-w
Select tappAS file to download below. Latest tappAS version available is 1.0.7.
| Application Files | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tappAS v1.0.7 | tappAS Application version 1.0.7 | Filesize: 17.856Mb | ||||||||||||
| Note: In tappAS 1.0.4 or newest you have to delete your last tappAS application (versions 0.99.15 or below) and its tappasWorkspace folder and create all the projects again. Thank you for your understanding. If you were working with your own annotation file, you can visit our Miscellaneous Files |
| install.pdf | tappAS Installation and Requirements | Filesize: 82.7K |
GFFs files | tappAS GFFs |
| If you would like to follow de [ISMB 2020 tutorial], you can find the example dataset here. | tappAS - ISMB 2020 tutorial data | Filesize: 6Mb |
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Note: You may download additional annotation files and demos from the application as needed.
| Releases | |
|---|---|
| 1.0.8 | Under development... |
| General -Now, transcript features with the genomic position are displayed correctly. -sQTL splice junctions are accepted and they are displayed in blue. -GO annotation has been updated (XXX). -Miscellaneous changes. | |
| 1.0.7 | April 5, 2021 |
| Analyses - Fixed DFI for Single Time series - Fixed DEA for Single Time series - FEA now has the option to select all the features in one click General -RBPs feature now are showed in Transcript View -GO annotation has been updated (February 01 2021). -Miscellaneous changes. | |
| 1.0.6 | January 8, 2021 |
| Analyses - Fixed DFI for Single Time series - Fixed DPA for Single Time series - Fixed UTRL for Single Time series -Miscellaneous changes. | |
| 1.0.5 | December 11, 2020 |
| General -Now, tappAS can manage projects without proteins. -Better insertion of TranscriptInformation if it is not present in the GFF3. -Miscellaneous changes. Analyses - Fixed DFI for Time series - Fixed DFI Gene visualization General -GO annotation has been updated (December 08 2020). | |
| 1.0.4 | October 10, 2020 |
| Analyses -Heatmap fixed in DPA. -UTRL Analysis fixed (minor error). -Labels fixed in Diversity Analysis. General -GO annotation has been updated (October 10 2020). | |
| 1.0.3 | August 3, 2020 |
| Analyses -DFI Summary plots fixed. Now can detect the features come from Transcript or Protein annotation correctly. -Minor DIU Analysis bug fixed when filter by proportion is used. | |
| 1.0.2 | July 23, 2020 |
| General -GO annotation has been updated (July 17, 2020). -Miscellaneous changes. Analyses -Minor DFI Analysis bug fixed. | |
| 1.0.1 | May 12, 2020 |
| General -GO annotation has been updated (May 2, 2020). -Miscellaneous changes. Analyses -DFI Analysis fixed for Time Course Experiments. | |
| 1.0.0 | March 6, 2020 |
| General -Install packages automaticatly updated. -Load projects it is now faster. -Updated all Help Documentation. -Updated Overview. -GO annotation has been updated (February 21, 2020). -URLs updated to work with the new website. -Minor bugs fixed. -Miscellaneous changes. Analyses -DEA for time-course analysis fixed. -DFI Summary tables fixed. -Co-DFI updated. -Violin plot in UTRL analysis fixed. -FEA clustering fixed. -GSEA clustering fixed. -New Enriched Feature visualization in GSEA. | |
| 0.99.15 | September 25, 2019 |
| General -Experiment type "Case-Control" now is called "Two-Group Comparison". -Fixed DFI Result Summary drillDown option. -New UTR Lengthening Analysis (UTRL). -New R packages installation. -Fixed R graphics in Windows computers. -Fixed FDA graphics. -Updated DPA Analysis (Now it works for genes with multiple isoforms and no NDM transcripts). -Updated DPA HeatMap (Two-Group Comparison). -Updated all JavaFX visualizations. -Updated help dialogs. -Updated Overview. -GO annotation has been updated (July 1, 2019). -Miscellaneous changes. Time Course Experiments -Minor correction in FDA. -Now, DEA analysis shows P-Value and R square as a columns. -Now, you can export ranked list in DEA analysis. -Fixed DFI Graphics. -Fixed DPA Graphics. -Now, GSEA allows you to select our own tappAS ranked lists. -Fixed GSEA mdgsa. -Minor bugs fixed. | |
| 0.99.14 | June 28, 2019 |
| -Now if a transcript is NMD, it won't shown protein. -New R visualization packages added to tappAS. -Fixed: tappAS couldn't load a custom project if you modified .gff file. -Miscellaneous changes in all graphs (title size, axis...) and export quality. -New FDA Combined ID Results (New combined FDA ID analysis when you run for the same Feature, the analysis with Genomic Position and Presence parameters.) -New FDA Combined Results Summary. -Now, DEA and DIU Combined results show switching in transcripts and proteins. -Fixed DIU graph. -Fixed DPA values in annotation files. You have to download again all the annotation and create the projects to work correctly. -New DPA graph to compare DPAU between conditions. -Fixed DFI for Time series. -Fixed DFI gene visualization. -Fixed FEA Summary Graph. -Added new option to FEA Summary (at left-hand side menu). -Now, FEA Analaysis can be run for multiple features. -New, GSEA method (mdgsa). -New, GSEA multivariant method (mdgsa) for GOTerms. -New, GSEA multivariant Interactive Summary. (You can see how much a GOTerm is regulated by each ranked list.) -Fixed GSEA search. -Fixed, if you select don't normalize your data you can't run edgeR method in DEA. (Because need raw data and we can't verify your data is not already normalized). -Now, when you export a graph, the gene name will be show in the name file. -Fixed in all annotations miRNA feature by miRNA_Binding. -Fixed add extra columns by ID or Description in each table. -GO annotation has been updated (June 25, 2019). | |
| 0.99.13 | May 29, 2019 |
| -Now, if there is a new version of tappAS you will be notified. -Some GFF features have been renamed. -Creating a new project, not integer values are suported in CPM filter. -Now, you can select if you want to normalize your expression matrix by TMM method. -FDA can store different analysis results. -Now, FDA support two kind of analyses. Collapsing by feature or by id. -FDA graph has been improved. -Fixed sorted of FDA columns. -Fixed DEA. Now, if you chose NoiSeq method you can indicate your own Fold Change to consider differential expression. -Now in DEA, you can show the number of isoforms column. -DIU pie chart indicates percentage of major switching isoforms. -Fixed DIU graph. Now the top 5 genes are labeled correctly. -DFI can store different analysis results. -Fixed DFI filter. -DFI Gene Associations change to Co-DFI Associations. -Fixed DPA Log2(FC) graph. -Now, Genomic Position comparation works correctly in FDA and DFI. -Now, in FDA and DFI analyses you have to choose to analyze by Genomic Position or Presence, and the features you can analyze change depending its nature. -Structual_Information source has change to TranscriptAttributes. -Fixed graph: Transcripts, Protein and Gene Per Chromo. -GO annotation was update (May 9, 2019). -Miscellaneous changes. | |
| 0.99.12 | February 18, 2019 |
| -Now, you can download all the R packages you need automatically. -Now, you can copy transcript, protein, genomic and expression charts images to clipboard. -New Demo with extra annotations. -New FDA graph. -New DPA expression columns. -New DPA graph in DPA summary. -Disable MDGA mehotd in GSEA. -Replacing TotalChg column by Total Usage Change in DIU Analysis. -Fixed DIU scatter plot. -Fixed DPA Plot (Log2 Fold Change). -Fixed GSEA parameter windows for low resolution screens. -Minor correction in FEA (Combobox names). -Minor correction in FDA (Graphs). -Minor correction in DPA (Graphs). -Minor correction in DFI (Graphs). -GO annotation was update (February 17, 2019). -Miscellaneous changes. | |
| 0.99.11 | January 07, 2019 |
| -New using method in DFI analysis (old Genomic is totally update). -New summary graphics in DFI analysis for Case-Control experiment. -Fixed DFI filtering. -Fixed DPA analysis. -Minor correction in DPA analysis (graphs and names). -Modify TotalChange column by ΔDPAU (distal polyA usage) and ΔFI (feature inclusion). -Minor correction in General Summary. -GO annotation was update (December 28, 2018). -Miscellaneous changes. | |
| 0.99.10 | November 23, 2018 |
| -Minor DPA bugs fixed. -Now, Podium Change is named as Mayor Isoform/PolyA Switching. -Now, DSA is named as Differential Isoform Usage (DIU). -Now, FDSA is named as Differential Feature Inclusion (DFI). -Added new filters in DIU, DFI and DPA (by fold change or proportion). -Fixed color in NMD transcripts. -The method edgeR was eliminated from DIU, DFI and DPA. -GO annotation was update (October 25, 2018). -Miscellaneous changes. | |
| 0.99.09 | October 11, 2018 |
| -Now, NMD transcripts are a different color. -Changed colors visualization in transcripts and proteins. -Fixed values of error marks. -Fixed ordering in proteins and transcripts. -Fixed multiple time series charts in DPA. | |
| 0.99.08 | September 18, 2018 |
| -Error marks added to Expression Charts. -Now, you can run the Functional Diversity Analysis for a specific list of genes. -Added DPA Gene Summary option. -Minor correction in FEA. -Minor correction in GSEA. -Fixed image exportation for DPA and DEA clusters. -Fixed column size in all analysis to show all the title. -Fixed Protein name for CDS. -Fixed visualization subtaps (Now, you can't see the same symbol for different sources). | |
| 0.99.07 | July 20, 2018 |
| -New Differential PolyAdenilation Analysis (DPA) -New annotations files with structure information -New background white color for all graphics -New set of color for all graphics and new icon design -Minor Podium Change bugs fixed -Minor FDSA bugs fixed -Minor FEA bugs fixed -Minor DEA bugs in Case-Control fixed -Miscellaneous changes | |
| 0.99.06 | March 23, 2018 |
| -Implemented new GSEA method to run analysis (MDGSA) -Implemented new automatic filtering and reduction for GOterms in GSEA and FEA -Implemented Favored condition -Fixed filter in DSA and FDSA -Fixed FDSA features selection -Fixed save chart in FDSA drill down -Added information to run tappAS If your hardware are much lower than recommended -Automatically save the directory for rankList in GSEA and FEA for next time -Miscellaneous changes | |
| 0.99.05 | February 20, 2018 |
| -Implemented DSA for single and multiple series time-course -Implemented FDSA for single and multiple series time-course -Implemented Podium Change for DSA and FDSA -Fixed Expression Values Filter when you create a new project -Miscellaneous changes | |
| 0.99.04 | February 07, 2018 |
| -Viewing gene online reference feature not available for user annotation files -Fixed "abort function" in almost all analysis -Fixed expression charts icon -Miscellaneous display theme changes | |
| 0.99.03 | February 05, 2018 |
| -Automatically save the directory of all data for next time -Using new format for project parameters -Miscellaneous internal changes -Miscellaneous display theme changes | |
| 0.99.02 | January 26, 2018 |
| -Fixed display of tab overflow names in tab pane menu -Fixed protein sort by expression level in gene data visualization -Modified about dialog to show credits -Miscellaneous display theme changes | |
| 0.99.01 | December 15, 2017 |
| -Initial release of TAPPAS after name change from Transcript2GO - will use new tappasWorkpsace folder |
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